Mechanisms of Inherited Epigenetic Dysregulation in Early Embryonic Development

一个主要的重编程波重置了早期胚胎的全基因组DNA甲基化谱。然而，我们最近发现的有限数量的重要序列和新区域必须逃避这些动态变化，并通过连续的DNMT 1（DNA甲基转移酶1）活性维持精确的DNA甲基化谱。这些DNA甲基化标记的不忠实传递导致遗传性表观遗传失调（表观遗传错误的细胞间传递），这反过来可能是调控网络异常背后的病因学的一部分。 在DNMT 1依赖性DNA甲基化维持丧失后，遗传性表观遗传失调是如何出现的？为了解决这个问题，我们开发了一个转基因胚胎干细胞（ES）模型与诱导Dnmt 1抑制复制胚胎去甲基化和再甲基化波没有任何DNMT 1依赖的维护活动。 我们的主要假设：在早期胚胎程序中表观遗传特征的失调将引起一系列特定的表观遗传扰动，导致异常的表观遗传适应，阻止DNMT 1维持特征。使用下一代测序方法，我们将在我们创新的Dnmt 1 tet/泰特ES细胞模型中建立DNA甲基化和组蛋白修饰的综合表观遗传图谱。 我们的三个目标是： 1-描述Dnmt 1 tet/泰特ES细胞中全基因组去甲基化和再甲基化过程中DNMT 1依赖性DNA甲基化的动力学。通过在DNMT 1依赖性甲基化的丧失和重建过程中建立全基因组DNA甲基化动态，我们将为清晰理解遗传性表观遗传失调背后的机制奠定基础。 2-定义DNMT 1依赖性甲基化谱完全丧失和重建过程中组蛋白表观遗传景观的适应性反应。我们建议确定DNA甲基化谱的暂时丢失是否会触发特定组蛋白修饰的永久重排，这将阻碍结合因子在具有遗传表观遗传失调的序列上招募DNMT 1。 3-确定在Dnmt 1 tet/泰特ES细胞中诱导遗传失调后，表观遗传景观中的特定适应是否阻止初始表观遗传特征的恢复。利用生物信息学，我们将交叉检查DNA甲基化（目标1），组蛋白标记和相关的DNA结合因子（目标2）的数据，以确定特定的表观遗传相互作用，解释遗传表观遗传失调的机制。 我们的计划将回答有关胚胎细胞中遗传表观遗传失调的机制问题，这些问题在其他系统中仍然难以捉摸，进一步建立Dnmt 1 tet/泰特ES细胞作为该领域的重要模型。

A major reprogramming wave resets genome-wide DNA methylation profiles in early embryos. However, a limited number of important sequences and novel regions that we recently identified must escape these dynamic changes and sustain precise DNA methylation profiles through continuous DNMT1 (DNA methyltransferase 1) activity. Unfaithful transmission of these DNA methylation marks leads to inherited epigenetic dysregulation (cell-to-cell transmission of epigenetic errors), which in turn could be part of the etiology behind abnormalities found in regulatory networks. How does inherited epigenetic dysregulation emerges following a loss of DNMT1-dependent DNA methylation maintenance? To address this question, we developed a transgenic embryonic stem (ES) cell model with inducible Dnmt1 repression to reproduce the embryonic demethylation and remethylation waves without any DNMT1-dependent maintenance activity. Our main hypothesis: Dysregulation of epigenetic profiles in an early embryonic program will provoke a cascade of specific epigenetic perturbations, leading to abnormal epigenetic adaptation that prevents DNMT1 from maintaining profiles. Using next-generation sequencing approaches, we will establish comprehensive epigenetic maps for DNA methylation and histone modifications across the loss and regain of DNA methylation in our innovative Dnmt1tet/tet ES cell model. Our three aims are: 1- Delineate the kinetics of DNMT1-dependent DNA methylation throughout the process of genome-wide demethylation and remethylation in Dnmt1tet/tet ES cells. By establishing genome-wide DNA methylation dynamics during the loss and reestablishment of DNMT1-dependent methylation, we will set the foundation for a clear understanding of the mechanisms behind inherited epigenetic dysregulation. 2- Define the adaptive response in the histone epigenetic landscape during the course of complete loss and reestablishment of DNMT1-dependent methylation profiles. We propose to determine if temporary loss of DNA methylation profiles triggers permanent rearrangements in specific histone modifications that would impede binding factors to recruit DNMT1 on sequences bearing inherited epigenetic dysregulation. 3- Determine if specific adaptations in the epigenetic landscape prevent the recovery of initial epigenetic profiles following induced inherited dysregulation in Dnmt1tet/tet ES cells. Using bioinformatics, we will cross-examine data on DNA methylation (Aim 1), histone marks, and related DNA binding factors (Aim 2) to identify specific epigenetic interactions that explain mechanisms implicated in inherited epigenetic dysregulation. Our program will answer mechanistic questions about inherited epigenetic dysregulation in embryonic cells that have remained elusive in other systems, further establishing Dnmt1tet/tet ES cells as an important model in this field.